An evo-devo geek's scientific meanderings

Month: January 2012

Richard Lenski’s team is one of my favourite research groups in the whole world. If the long-term evolution experiment with E. coli was the only thing they ever did, they would already have earned my everlasting admiration. But they do other fascinating evolution stuff as well. In their brand new study in Science (Meyer et al., 2012), they explore the evolution of a novelty – in real time, at single nucleotide resolution.

For their experiments, they used a pair of old enemies: the common gut bacterium and standard lab microbe E. coli, and one of its viruses, the lambda phage. Phages (or bacteriophages, literally “bacterium eaters”) are viruses that infect bacteria. They are also some of mother nature’s funkiest-looking children. Below is an example, because if you haven’t seen one of them, you really should. I borrowed this electron micrograph of phage T4 from GiantMicrobes, where you can get a cute plushie version 😛

Phages work by latching onto specific proteins in the cell membrane of the bacterium, and literally injecting their DNA into the cell, where it can start wreaking havoc and making more viruses. Meyer et al.‘s phage strain was specialised to use an E. coli protein called LamB for attachment.

The team took E. coli which (mostly) couldn’t produce LamB because one of the lamB gene’s regulators had been knocked out. Their virus normally couldn’t infect these bacteria, but a few of the bacteria managed to switch lamB on anyway, so the viruses could vegetate along in their cultures at low numbers. Perfect setup for adaptation!

Meyer and colleagues performed a lot of experiments, and I don’t want to go into too much detail about them (hey, is that me trying not to be verbose???). Here are some of their intriguing results:

First, the phages adapted to their LamB-deficient hosts. They did so very “quickly” in terms of what we usually think of as evolutionary time scales (naturally, “evolutionary time scales” mean something different for organisms with life cycles measurable in minutes). Mutations in the gene coding for their J protein (the one they use to attach to LamB) enabled them to use another bacterial protein instead. Not all experimental populations evolved this ability, but those that did succeeded in less than 2 weeks on average.

The new protein target, OmpF, is quite similar to LamB, which might explain how the viruses evolved the ability to use it so quickly. But more interesting than the speed is the how of their innovation. Amazingly, all OmpF-compatible viruses shared two specific mutations. Another mutation always occurred in the same codon, that is, it affected the same amino acid in the J protein. A fourth mutation invariably occurred in a short region near the other three. Altogether, these four mutations allowed the virus to use OmpF. Plainly, we are dealing with more than mere convergent evolution here. Often, many different mutations can achieve the same thing (see e.g. Eizirik et al., 2003), but in this case, a very specific set of them appeared necessary. I’ll briefly revisit this point later, but first we have another fascinating result to discuss!

By comparing dozens of viruses that did and didn’t evolve OmpF compatibility, the researchers determined that all four mutations were necessary for the new ability. Three were not enough; there were many viral strains with three of the four mutations that couldn’t do anything with LamB-deficient bacteria. On the surface, this sounds almost like something Michael Behe would say (see Behe and Snokes, 2004), except the requirement for more than one mutation clearly didn’t prevent innovation here. Given the distribution of J mutations, it’s also likely that they were shaped by natural selection, even in virus populations that didn’t evolve OmpF-compatibility. So what did the first three mutations do? What use was, as it were, half a new J protein?

The answer would delight the late Stephen Jay Gould: the new function was a blatant example of exaptation. Exaptations are traits that originally had one function, but were later co-opted for another. While three mutations predisposed the J gene to OmpF-compatibility, they also improved its ability to bind its original target. Thus, there was a selective advantage right from the first mutation. And, in essence, this is what we see over and over again when we look at novelties. Fish walk underwater, non-flying dinosaurs cover their eggs with feathered arms, and none of them have the first clue that their properties would become success stories for completely different reasons.

In the paper, there is a bit of discussion on co-evolution and how certain mutations in the bacteria influenced the viruses’ ability to adapt to OmpF, but I’d like to go back to the convergence/necessity point instead. I have a few half-formed thoughts here, so don’t expect me to be coherent 😉

We’ve seen cases where the same outcome stems from different causes, like in the cat colour paper cited above. Then there is this new function in a virus that seems to always come from (almost) the same set of mutations. Why? I’m thinking it has to do with (1) the complexity of the system, (2) the type of outcome needed.

Proteins interact with other proteins through very specific interfaces. Sometimes, these interactions can depend on as little as a single amino acid in one of the partners. If you want to change something like that, there is simply little choice in what you can do without screwing everything up. On the other hand, something like coat colour in mammals is controlled by a whole battery of genes, each of which may be amenable to many useful modifications. And when it comes to even more complex traits like flying (qv. aside discussing convergence and vertebrate flight/gliding in the mutations post), the possibilities are almost limitless.

So there’s that, and there is also what you “want” with a trait. There may be more ways to break a gene (e.g. to lose pigmentation) than to increase its activity. When the selectively advantageous outcome is something as specific as a particular protein-protein interaction, the options may be more restricted again. (To top that, the virus has to stick to the bacterium with a very specific part in its structure, or the whole “inject DNA” bit goes the wrong way.) Now that I read what I wrote that sounds like there will be very few “universal laws” of evolutionary novelty (exaptation being one of them?). Hmm…

A bit belatedly, but as the Cambrian mammal, I feel it’s my duty to jump on the Siphusauctum bandwagon. I was actually a bit surprised by how much news and blog coverage the creature got. I didn’t expect something with no clear affinities to anything and no particularly “cool” features of its own to make many headlines. It’s just a peaceful filter-feeder that looks like a mutant tulip, FFS.

Guess I fail the internet?

Below is a nice bouquet of tul… I mean, Siphusauctum fossils on their slab of rock, from O’Brien and Caron, 2012. They are completely soft-bodied creatures that range from under 2 cm to more than 20 in total height. Presumably, the live animals stood upright on their thin stalks and filtered food particles from the water. The authors speculate that they may have been able to move from one spot to the other, because the small holdfasts at the end of the stalk don’t seem like strong, permanent anchors.

I don’t particularly want to dwell on the details of the paper. It’s the dry and tedious sort of thing descriptions of new taxa usually are, and all those news and blog articles probably beat me to all the basics as far as explaining the animal to a lay audience goes. I just want to make a couple of totally random observations.

One – how the hell do they know that the creature had a mouth? The authors seem quite certain that the digestive tract of Siphusauctum had both a mouth and an anus, but as far as I can tell, they only actually found one hole (which they interpreted as the anus). The mouth is only mentioned a few times, and the most information you get about it is this:

The precise position of the mouth is unknown but was presumably located around the area between the base of the comb-like segments and the stomach. (p16 in the PDF)

and this:

Food particles would have circulated down towards the gut, through a central mouth which has not been identified, but is suggested by the concentration of organic matter in this area. (p18)

Someone please explain why that implies a separate mouth? I mean, they found well over a thousand specimens of not too bad quality. These people have a few thousand times more expertise than me in interpreting weird Cambrian fossils. I would assume they didn’t pull the idea out of thin air, but they don’t exactly make it convincing for non-specialists there 😦 (Not that a single-opening digestive tract makes the animal any easier to interpret…)

Two – Siphusauctum apparently has sixfold symmetry. I don’t know if that’s significant, it just struck me as something that isn’t terribly common in living bilaterians. Hard corals and sea anemones work in multiples of six, but they aren’t bilaterians. But maybe I should go check a zoology textbook…

Three – I found it funny that in true Cambrian style, the creature most similar to Siphusauctum is… Dinomischus? Which is another weird Burgess Shale fossil no one can really place. Well, at least now they have company in being complete riddles. 😀

Or how I learned (again) that there are no truly simple stories in biology.

In the name of fairness and plain old intellectual integrity, I should mention some interesting new developments in the treehopper-helmet-novelty issue. Back in the first treehopper post I acknowledged that I’m a far cry from an entomologist, and a new study argues that Benjamin Prud’homme and the entire crew on Prud’homme et al. (2011) may share that attribute with me.

A paper published recently in the open-access online journal PLoS ONE (Mikó et al., 2012) questions basically every interpretation the previous study made about those funky thoracic appendages. After dissecting, CT-ing and microscoping several treehoppers and related insects, they conclude that:

The helmet is not an appendage that articulates with the first thoracic segment – it’s actually most of the first thoracic segment itself.

The joint at the base of the helmet is the articulation between the first two thoracic segments.

The paired “helmet buds” Prud’homme et al. reported are more likely to be artefacts of the way they sectioned their specimens, since Mikó et al. couldn’t find any in treehoppers of a similar developmental stage.

If all of this is correct, that would suggest that the helmet has nothing to do with wings, it’s just like other less extreme outgrowths of the thorax that you find in a large variety of insects.

What about the genes?

If you take a gander at the first treehopper post or Prud’homme et al. (2011) itself, you’ll see that they supported their microscopic observations with gene expression data including two appendage-specific genes and one that they considered specific to wings. However, even I had a note of caution about using Dll/Dlx genes – which seem to be there whenever anything starts sticking out of an animal’s body – as evidence of homology to anything. Mikó et al. (2012) point out that nubbin, the supposed “wing gene” actually has quite variable roles in wing and other appendage development when you look at more insect species besides fruit flies. The Hth-Dll combo, it appears, is also involved in the development of more obviously non-wing thoracic outgrowths, like beetle horns.

Where does that leave us?

Seeing as I’m still no entomologist, I can’t really take sides in the anatomical arguments. The genetics? What immediately springs to my mind is Keys et al. (1999), and how some butterflies grow their eyespots by the wholesale co-option of a genetic regulatory circuit from wing development. Did the same sort of thing happen to beetles and treehoppers, then?

This, in fact, only reinforces my general opinion about novelties and the nature of genetic evidence. Evolution rarely, if ever, works from scratch, and the boundary between “novelty” and “tinkering” is as blurry as it gets. Thus, “homology” is rarely a clear-cut and straightforward issue. All of that still stands [1], even if treehoppers might have shifted on some sliding scales. (Which direction is an interesting question. Is a re-activated wing homologue more or less “novel” than a generic thoracic outgrowth patterned by some wing circuitry? Does the distinction even make sense?)

All in all, this is getting quite interesting. It feels decidedly like the beginning of a heated debate [2]. I’ll certainly keep an eye out for future episodes of the treehopper saga.

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[1] Though I have to say, I have a couple of papers on my reading list that may mess with my opinions… Don’t want to jinx it, so I won’t say more, but I’m hoping to make a post out of them one day.

I’m talking mostly to myself in this one, but do listen if you want to know the random questions crossing a trainee evolutionary scientist’s mind 🙂

So, when you work with DNA or protein sequences, you learn that you should be careful with repetitive sequences. For example, here is a protein that consists mostly of the same amino acid (D = aspartic acid, in case you wondered) over and over again:

It’s a protein found in oyster shells, but it could be anything, the problem remains the same. You learn that when you compare/align sequences, you shouldn’t base an alignment, or conclude that two sequences are homologous, on bits like the above. (Which didn’t prevent some people from saying that this very protein “shows homology to” something else)

I kind of never questioned that, but really, why?

We humans are intuitively bad at probability, but when you think about it, a series of sixty Ds is just as likely as a pitch-perfect homeodomain. It’s like coin tossing. When every throw has a 1/2 chance of landing heads *or* tails, then any particular sequence of heads and tails is equally likely. HHHH and HTHT are exactly equally probable.

Nucleotides or amino acids are slightly different, because not all letters are equally likely, but the rarer ones can also form repeats, and I don’t think I’ve ever heard anyone make an exception for them.

My best guess is that repeats are easy to make by some sort of DNA replication slippage, so they come and go in evolution as they please. Does that make sense?

I think I have to go and ask someone…

ETA: Hmm, it appears to be a computational issue, based on the BLAST guides over at NCBI. Sayeth the Manual:

There is one frequent case where the random models and therefore the statistics discussed here break down. As many as one fourth of all residues in protein sequences occur within regions with highly biased amino acid composition. Alignments of two regions with similarly biased composition may achieve very high scores that owe virtually nothing to residue order but are due instead to segment composition. Alignments of such “low complexity” regions have little meaning in any case: since these regions most likely arise by gene slippage, the one-to-one residue correspondence imposed by alignment is not valid. While it is worth noting that two proteins contain similar low complexity regions, they are best excluded when constructing alignments [42-44]. The BLAST programs employ the SEG algorithm [43] to filter low complexity regions from proteins before executing a database search.

So… yes, part of it is replication slippage, but also, the… low complexity of low-complexity regions skews the probability calculations. If you base your match probabilities on the assumption that only every 20th amino acid is an aspartate, and in your sequence it’s every 2nd or 3rd, the match will seem far less likely than it would if you used the real composition of your sequence.

That makes sense. The Mammal is unconfused and feeling kind of smug now 🙂

Back when Star Wars was new – and even when the new trilogy was new -, a planet orbiting more than one star was nothing more than speculation. (Though back when SW was new, even a planet orbiting another star was little more than speculation.)

I’m excited to see that the Kepler team are busy turning it into solid reality. They now have not one, not even two, but three planets that they found around binary stars (the first was described a few months back [Doyle et al., 2011]; the other two are just online [Welsh et al., 2012]). None of them are particularly Tatooine-like, alas, since all are gas giants, but given how hard small planets are to find, we can be fairly confident that we’ve just overlooked them so far.

All three planets orbit in the same plane in which their stars orbit each other, indicating that the whole system formed from the same rotating disc of space debris. Based on the number of star pairs they’ve looked at so far and the chance of observing planetary transits in binary systems like Kepler-16, 34 and 35, Welsh et al. estimate that millions of similar systems could be hiding in the Milky Way alone.

To top it off, another new Nature paper (Cassan et al., 2012) reports that in fact, most sun-like stars in the galaxy are likely to have planets.

A truly astronomical number of strange new worlds are out there. How many of them could harbour life?

(Can you hear my inner geek squealing with joy? :D)

***

References

Cassan A et al. (2012) One or more bound planet per Milky Way star from microlensing observations. Nature481:167-169

(I’m even further behind on things than usual, so this is not that “hot” off the press, but the walking lungfish can’t not be posted on.)

The evolution of new traits serving new functions is always a bit of a chicken and egg problem. Why would you need wings if you don’t fly, and how could you start flying without them? Why would you need legs if you don’t walk, and how would you walk without legs?

Often, as in the case of wings, the most likely answer is that the trait originally had a different function that didn’t necessitate a “perfect” version of it. Wings that are no good for flying could be anything from egg-warmers/shades through mate attraction devices to balancing organs for prey-wrestling predatory dinosaurs (latter idea from Fowler et al., 2011, which by now has probably gone as viral as scientific papers can).

With legs, though, it seems that the chicken really did come first. We’ve known for a long time that coelacanths (which are somewhat distantly related to vertebrates with legs) sometimes move their pectoral and pelvic fins in an alternating rhythm that resembles walking. (IIRC you can find a fair few YouTube videos in which they are filmed doing that.) Nonetheless, coelacanths use this movement for swimming. They don’t actually get down and plod along the bottom.

Just to be clear, the animal in question is the West African lungfish (Protopterus annectens). Unlike the respectable paddles of the Australian species, its spindly paired appendages barely even deserve to be called fins, let alone legs. (Drawing below from King et al., 2011)

Yet this creature uses its pelvic fins to propel itself along the bottom in a variety of ways. It can walk with alternating “steps”, it can bound by moving both fins at once, and sometimes it just ambles along in a slightly irregular way (videos here). If there’s no traction on the bottom of the tank, it slips and can’t get anywhere, which indicates that it does indeed propel itself by pushing against the bottom with its hind fins. And sometimes, when the fins push off, you can see part of the body come clear off the ground.

(Interestingly, the lungfish walks and bounds only with its hind fins. Meanwhile, the pectorals flail around doing other things, but they don’t engage with the floor. The diagram above gives a clue why: the animal has huge, air-filled lungs – the grey blob – that help its front half float. It doesn’t need its forefins to stroll around.)

Given how un-leglike the fins of African lungfish are, it is obvious that walking underwater doesn’t require anything as sophisticated as ankles or toes or, heck, even proper fins. Just about any ancient lobe-finned fish we know could have been capable of it. Could this be how our ancestors took their first unknowing steps towards land? Were they bottom-dwelling fish that patrolled their territories in a stately fin-walk? Did increasingly leg-like fins just help them do that better rather than breaking new ground? As the authors remind us, we already know that many of the earliest tetrapods – creatures with true legs – lived in water. If less tetrapod-like creatures could walk, then the picture fits quite nicely together.

And speaking of chickens and eggs, once again nature proves how much human incredulity is worth. Just because you don’t know what to do with half a wing, just because you don’t think X is possible without Y, doesn’t mean solutions don’t exist. Studying nature is a life-long lesson in humility in that way.

***

References:

Fowler DW et al. (2011) The predatory ecology of Deinonychus and the origin of flapping in birds. PLoS ONE6:e28964

King HM et al. (2011) Behavioral evidence for the evolution of walking and bounding before terrestriality in sacropterygian fishes. PNAS108:21146-21151

I love BBC documentaries. I also used to love the books of David Attenborough’s BBC documentaries (I never watched those. I know, shame on me.). They tend to have the same sense of wonder that drove me to natural science, and which is lost in a number of other documentaries I’ll refrain from naming for now.

I understand that you can’t show all the subtleties and uncertainties and bloody wars over pet hypotheses that characterise cutting-edge science in a work aimed to entertain as well as educate the public. To tell a coherent and engaging one-hour story, you must simplify.

That doesn’t mean your story has to be bullshit.

(FWIW, my first beef is with the title of the film. It’s called First Life, but it gallops through the 80% of life’s history that didn’t involve animals in like the first ten minutes of the two-hour run time. But I digress.)

You see, in the first part, we get a nice lead-up to the Cambrian explosion, starting with Snowball Earth, the origin of multicellularity, animals (enter sponges), body plans (enter Ediacaran creatures), and so on. At some point, there is some musing about how complex animals began to diversify and adapt to new lifestyles, and it’s brought down to… the increased genetic variation provided by sex.

(ETA 120121: I should clarify, because I was having a bit of a brain fart when writing the original rant. The Marinoan glaciation, where my Snowball Earth link leads, is NOT the last big glaciation before the advent of animals. That honour would probably go to the Gaskiers glaciation, which I’d completely forgot was later than the Marinoan – roughly the same age as early Ediacaran fossils, in fact. Nonetheless, Wikipedia reassures me that the Gaskiers was not as severe as hardcore snowball events like the Marinoan.)

It’s pretty clearly implied by the narration that animals began to reproduce sexually around the time they started moving about and having heads and tails and similar complexities. If you paid attention to the story they were telling you up to that point, you can come away thinking that earlier animals didn’t get it on. (Like sponges don’t???)

The only problem with this is that it’s 99.999% certainly, utterly, and obviously, wrong. Sexual reproduction[1] is an ancestral feature of eukaryotes, that is animals, amoebae, malaria parasites, plants, algae of all sorts, fungi, slime moulds, paramecia, etc. etc. (name your favourite protist).

Animals do it in fundamentally the same way, using fundamentally the same molecular machinery as other eukaryotes. And there is every indication that they always practised it. Sponges do it. I’m willing to bet that every major animal group does it. Sure, many animals are also quite happy to reproduce by budding or falling to pieces, but most of them are at least capable of sex. Very little is known about the life of our closest non-animal relatives, but the sexy genes are there.

So, um, that exciting story you were telling us about how sex changed everything? Doesn’t work. I suspect that the whole nonsense was stuffed in so that they could show off this cool find, but can’t you talk about the earliest evidence for animal sex without making it sound like something it isn’t?

Hrm. That kind of unmade my day. Now I worry if the same level of crap gets into the other documentaries I loved so much, and I just didn’t spot it because I’m not a physicist/mathematician/historian/insert profession here. Ah, the joys of being an insufferable pedant and watching films about stuff you actually have a passing acquaintance with…

[1] basically, the making and fusion of sex cells. Everything else, from testicles through frog hugs to intercourse, is just embellishment.